Oh, does it ever happen with other warpouts. Near as I can tell, all classes of ships are affected. It does kind of spoil the immersion when the awe-inspiring Ravana warps out, only to do, well, this:

You can also see some Manticores back there; the fact that they're facing the "wrong way" leads me to believe that they have already passed the warp plane.
Here's one more taken a few seconds later, for kicks. The Ravana is completely through, but still visible.

Is a nightly build the same thing as the 3.6.13 version? I'll look around for it.
EDIT: All right, I found the nightly build thread, downloaded v3.6.13 Revision 6449 for OS X, and played the first mission of Vassago's Dirge again. Same issues.